Fix for ROOT-6262

proper handling of genreflex commands like
genreflex ../x86_64-slc6-gcc48-opt/dict/AthenaKernel/AthenaKernelDict_gen.h -o ../x86_64-slc6-gcc48-opt/dict/AthenaKernel --select=../x86_64-slc6-gcc48-opt/dict/AthenaKernel_selection.xml
with full path for header and destination.